RetrogeneDB ID: retro_opri_72

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_1863:38095..38536(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000016940
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNRPB
• Ensembl ID: ENSOPRG00000007459
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptides B and B1 [Source:HGNC Symbol;Acc:11153]

Sequence

>retro_opri_72
CCAAAGAATGCAAAGCAACCAGAGCATGCAGAAAAGCAGGTTTGGGGTCTGGTGTTGTTGCATGGGGAAAGCTTGTTATC
CATGACTGTTGAGGAGCCACTTTCCATACACACTGGCATTGCTCGGGTACCACTTGGTGACACTGCAGGAGGTCCTGTAG
TTGATAGGGCTGCCTGAAGAAATATATCAGCAGGGGCCCACTTCTCAAGTTCCTTCTGGATTAGTAGGCCTGTCTGAGGA
GTTGGGGGGCCATCATGGCAGTTAATGATTCCATAGGGAATAGCAATTAGAGCAGGTGCTGCGGTTGTTGCTACTGCCAG
CCTTTCTGGAGCCCAAACATAGTACCCATCAGGATAACGGATTTGAACTCTATCTATAGGCAGACTGACTTCTACCCCAG
AAATAACAGCACTACCACCTGGTATGAGAACACCAGCTGGG

Alignment

ORF - retro_opri_72 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.68 %
• Parental protein coverage: 51.06 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PKNSKQAEREEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQ
          PKN.KQ.E..EK.V.GLVLL.GE.L.SMTVE.P....TGIARVPL...AGGP...RAA.R.I.AG.....
Retrocopy PKNAKQPEHAEKQVWGLVLLHGESLLSMTVEEPLSIHTGIARVPLGDTAGGPVVDRAA*RNISAGAHF-S

Parental  APAGLAGPVRGVGGPSQQXXXXXXXGTVAAAA--ATASIAGAPTQYPPG-RAGPPPMGRGAPPPGMMGPP
          .......PV.GVGGPS.Q..........A.AA..ATAS..GA.T.YP.G.R......GR....P.....P
Retrocopy SSFWISRPV*GVGGPSWQLMIP*GIAIRAGAAVVATASLSGAQT*YPSG*RI*TLSIGRLTSTPEITALP

Parental  PGMRPPMG
          PGMR.P.G
Retrocopy PGMRTPAG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_72 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011353	1 retrocopy	retro_amel_1403,
Canis familiaris	ENSCAFG00000006693	3 retrocopies	retro_cfam_1268, retro_cfam_1773, retro_cfam_461,
Callithrix jacchus	ENSCJAG00000020971	2 retrocopies	retro_cjac_172, retro_cjac_1739,
Dasypus novemcinctus	ENSDNOG00000007896	2 retrocopies	retro_dnov_2060, retro_dnov_2471,
Erinaceus europaeus	ENSEEUG00000015568	3 retrocopies	retro_eeur_312, retro_eeur_434, retro_eeur_6,
Felis catus	ENSFCAG00000014447	2 retrocopies	retro_fcat_1788, retro_fcat_1960,
Microcebus murinus	ENSMICG00000016519	4 retrocopies	retro_mmur_1012, retro_mmur_1478, retro_mmur_546, retro_mmur_861,
Myotis lucifugus	ENSMLUG00000016951	1 retrocopy	retro_mluc_1725,
Mustela putorius furo	ENSMPUG00000009283	1 retrocopy	retro_mputfur_1153,
Nomascus leucogenys	ENSNLEG00000009206	1 retrocopy	retro_nleu_761,
Otolemur garnettii	ENSOGAG00000016149	4 retrocopies	retro_ogar_2197, retro_ogar_2841, retro_ogar_2918, retro_ogar_3236,
Ochotona princeps	ENSOPRG00000007459	2 retrocopies	retro_opri_697, retro_opri_72 ,
Pongo abelii	ENSPPYG00000010841	1 retrocopy	retro_pabe_2265,
Pteropus vampyrus	ENSPVAG00000017013	1 retrocopy	retro_pvam_289,
Tupaia belangeri	ENSTBEG00000010040	3 retrocopies	retro_tbel_1117, retro_tbel_1171, retro_tbel_2839,
Tarsius syrichta	ENSTSYG00000014498	2 retrocopies	retro_tsyr_45, retro_tsyr_719,